[REVIEW]: Pyrimidine: An algebra-inspired Programming framework for evolutionary algorithms

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@Freakwill@boisgera<!--end-editor-- Reviewers: @mmore500, @sjvrijn Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/60f6f831c3d0037e1aff4f5fa13bfaf5"><img src="https://joss.theoj.org/papers/60f6f831c3d0037e1aff4f5fa13bfaf5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/60f6f831c3d0037e1aff4f5fa13bfaf5/status.svg)](https://joss.theoj.org/papers/60f6f831c3d0037e1aff4f5fa13bfaf5)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mmore500 & @sjvrijn, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @boisgera know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @mmore500

📝 Checklist for @sjvrijn

editorialbot commented 3 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.36 s (495.3 files/s, 437204.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              2              0              0         100002
JavaScript                      13           4737           4760          17564
HTML                            17           1322             51          12167
Python                         111           2662           1421           5937
Markdown                        11            699              0           1563
CSS                              5            304             69           1291
TeX                              1             21              0            177
YAML                             5             19             27            106
reStructuredText                 6             94            183             97
DOS Batch                        1              8              1             26
TOML                             1              5              1             24
make                             1              4              7              9
INI                              1              0              0              2
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                           176           9875           6520         138966
-------------------------------------------------------------------------------

Commit count by author:

   294  William Song

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 1873

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 3 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-319-31204-0_9 is OK
- 10.1093/gji/ggad446 is OK
- 10.1088/1742-6596/1719/1/012102 is OK
- 10.1109/ICEC.1997.592270 is OK
- 10.1007/s00500-016-2474-6 is OK
- 10.21105/joss.01701 is OK

MISSING DOIs

- No DOI given, and none found for title: Adaptation in Natural and Artificial Systems
- No DOI given, and none found for title: DEAP: Evolutionary Algorithms Made Easy
- 10.1093/bioinformatics/btz470 may be a valid DOI for title: Scaling tree-based automated machine learning to b...
- No DOI given, and none found for title: typing — Support for type hints
- No DOI given, and none found for title: Numpy - The fundamental package for scientific com...
- No DOI given, and none found for title: A review on genetic algorithm: past, present, and ...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: API design for machine learning software: experien...
- No DOI given, and none found for title: GAMA: A General Automated Machine Learning Assista...
- No DOI given, and none found for title: Interpretable Machine Learning for Science with Py...
- No DOI given, and none found for title: Genetic Algorithm: Reviews, Implementations, and A...
- No DOI given, and none found for title: Evolutionary Optimization Algorithms: Biologically...
- No DOI given, and none found for title: neat-python
- No DOI given, and none found for title: Algebraic structure

INVALID DOIs

- None

mmore500 commented 3 months ago

Review checklist for @mmore500

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Freakwill/pyrimidine?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Freakwill) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

sjvrijn commented 2 months ago

Review checklist for @sjvrijn

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Freakwill/pyrimidine?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Freakwill) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

mmore500 commented 2 months ago

Some comments on the manuscript. I plan to follow up shortly on the software content.

Title block

Remove “These authors contributed equally” for one author.

Summary

add a space in “programming(OOP)”

Statement of need

citations to holland and katoch are missing
add a space in “genetic algorithm(GA)”
be perhaps “optimization” or “sophisticated” would be more appropriate than “intelligent” algorithms”?
Consider overviewing features/modules in the library around line 37 (end of statement of need )—— in addition to optimization algorithms: what’s in benchmarks, what chromosome models are implemented, what crossover models are implemented, etc.

Algebra-inspired programming

The advantage or purpose of the algebra-inspired approach is never directly stated. This should be explained more explicitly.
“In a typical Python implementation, …” [implementation of what?]
Prefer citations over hyperlinks (i.e., for NumPy)
The meaning of resp. is unclear
“discrepancy” should probably be “difference”
Around line 52, the mixing of Python syntax S[ ] with formal mathematical notation is a bit confusing.
How line 98, 99, and the following code segment relate to the preceding manuscript narrative is unclear (beginning with “Algebraically, there is no discrepancy between…”)

Figure 1:

— the twin y axis on right isn’t labeled — caption does not need to mention that plotting algorithms are not included in the library

Visualization:

Because visualization isn’t a core feature of the library, consider rewriting the visualization section to exclude the plotting and focus on history extraction. The majority of the example code in this section is generic boilerplate matplotlib.

An example to begin

The variables c, x w and W appearing in the display math are not defined in the text

Conclusion

In closing sentence,

GitHub doesn’t need to be linked
might mention software license
numerous examples [showing what?]

References

avoid citations to wikipedia
type hints do not need to be cited

Overall

The purpose of overriding _fitness should be mentioned in the accompanying text. The override of the // operator to denote size should also similarly explicitly explained.
there are several broken references (search the manuscript for “??”)

boisgera commented 2 months ago

Hi @Freakwill,

@mmore500 has made some comments/requests about your paper ~2 weeks ago (see https://github.com/openjournals/joss-reviews/issues/6575#issuecomment-2071073010)

Would it help if I transcribed these bullet points as checklists and register them as issues in your project repository?

mmore500 commented 1 month ago

Ran into an install issue, will resume my review once that is unblocked! (https://github.com/Freakwill/pyrimidine/issues/4)

boisgera commented 1 month ago

For the record, I have e-mailed the project author to make sure that the communication channels (this JOSS issue as well as the project issue) with him are open and asked him to try to publicly acknowledge the reviewer messages (even if the issue can't be adressed right away).

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

Some comments on the manuscript. I plan to follow up shortly on the software content.

there are several broken references (search the manuscript for “??”)

I use the following cross-references according to the docs of joss. But why dose it result in ???

A concise comparison between `pyrimidine` and several popular frameworks provided in \autoref{frameworks}, such as ....

: Comparison of the popular genetic algorithm frameworks. []{label="frameworks"}

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

@editorialbot commands

editorialbot commented 1 month ago

Hello @Freakwill, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

Freakwill commented 1 month ago

@editorialbot check repository

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.42 s (500.0 files/s, 411662.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              2              0              0         100002
HTML                            34           2670            102          24377
JavaScript                      18           4853           4929          18267
Python                         115           2788           1490           6169
CSS                              7            554            114           2269
Markdown                        11            740              0           1611
reStructuredText                10            171            328            185
TeX                              1             18              0            173
YAML                             5             19             27            106
DOS Batch                        2             16              2             52
TOML                             1              5              1             24
make                             1              4              7              9
INI                              1              0              0              2
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                           209          11838           7000         153247
-------------------------------------------------------------------------------

Commit count by author:

   315  William Song
     1  Matthew Andres Moreno

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 2091

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Freakwill commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

boisgera commented 3 weeks ago

I use the following cross-references according to the docs of joss. But why dose it result in ???
A concise comparison between `pyrimidine` and several popular frameworks provided in \autoref{frameworks}, such as ....

: Comparison of the popular genetic algorithm frameworks. []{label="frameworks"}

I see that you apparently still have some weird formatting in this line, I'll have a look.

boisgera commented 3 weeks ago

AFAICT the autoref{eq:container} issue should be solved if you use the syntax

\begin{equation} \label{eq:container}
s = \{a:A\}: S \quad \text{or} \quad s:S[A] 
\end{equation}

boisgera commented 3 weeks ago

autoref{history} already works as expected :+1:

boisgera commented 3 weeks ago

And with respect to autoref{frameworks}, the caption

: Comparison of the popular genetic algorithm frameworks. \label{frameworks}

shoud appear after the table, not before. These are the three uses of autoref that I can find in the paper.

Freakwill commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

openjournals / joss-reviews